RNA-Seq study of small follicles and large follicles in Indian Ghoongroo pigs
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ABSTRACT:
PROVIDER: PRJNA951634 | ENA |
REPOSITORIES: ENA
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Project description:To gain insight into the differentially expressed genes (DEGs) and signalling pathways regulating development of small follicles (SF diameter ≥3 mm to <6 mm) into large follicles (LF diameter ≥6 mm) in Ghoongroo pigs, a comprehensive transcriptome profiling of porcine follicles was conducted using NovaSeq600 sequencing platform. The DEGs were identified using DESeq2 with threshold of padj <0.05 and log2 Fold Change cut off 0.58. Functional annotations and bioinformatics analysis of the DEGs were performed to find out biological functions, signalling pathways and hub genes regulating follicular development and function.
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Project description:Three different stages of pig antral follicles have been studied in a granulosa-cell transcriptome analysis on nylon microarrays (1152 clones). The data have been generated from 7 RNA follicle pools and several technical replicates were made. Four Large, one Medium and two Small follicles pools were considered. For each follicle pool, 2 radioactive labellings were performed. Each membrane was exposed 16 hours (to avoid saturation of the signal of highly expressed genes) and 28 hours (to get some signal from lowly expressed genes). Each probe was hybridised on GPL3971 scag_scai Sus scrofa 1.2K mono array and on GPL3970 scag_scai Sus scrofa 4.6K triplicate array (except for GFS2172 which was labelled only once and hybridised onto 2 GPL3971 scag_scai Sus scrofa 1.2K mono array membranes), so that 4 spots are available for each gene (and 2 spots for GFS2172), for a given RNA and a given radioactive labelling. Keywords: granulosa-cell transcriptome analysis data consisted in (6 RNA x 2 labellings) + (GFS2172 RNA X 1 labelling)= 13 probes, 26 hybridisations, 52 images.
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